Tools

"... The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The ..."

. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment

"... PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which ..."

phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil

"... Abstract-Speech recognition is formulated as a problem of maximum likelihood decoding. This formulation requires statistical models of the speech production process. In this paper, we describe a number of sta-tistical models for use in speech recognition. We give special attention to determining the ..."

"... This paper examines the application of linear transformations for speaker and environmental adaptation in an HMM-based speech recognition system. In particular, transformations that are trained in a maximum likelihood sense on adaptation data are investigated. Other than in the form of a simple bias ..."

This paper examines the application of linear transformations for speaker and environmental adaptation in an HMM-based speech recognition system. In particular, transformations that are trained in a maximumlikelihood sense on adaptation data are investigated. Other than in the form of a simple

"... Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called ..."

Two approximate methods are proposed for maximumlikelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called

"... Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version ..."

5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximumlikelihood (ML

"... Hidden Markov models (HMMs) are a powerful probabilistic tool for modeling sequential data, and have been applied with success to many text-related tasks, such as part-of-speech tagging, text segmentation and information extraction. In these cases, the observations are usually modeled as multinomial ..."

as multinomial distributions over a discrete vocabulary, and the HMM parameters are set to maximize the likelihood of the observations. This paper presents a new Markovian sequence model, closely related to HMMs, that allows observations to be represented as arbitrary overlapping features (such as word

"... The concept of maximum entropy can be traced back along multiple threads to Biblical times. Only recently, however, have computers become powerful enough to permit the widescale application of this concept to real world problems in statistical estimation and pattern recognition. In this paper we des ..."

The concept of maximum entropy can be traced back along multiple threads to Biblical times. Only recently, however, have computers become powerful enough to permit the widescale application of this concept to real world problems in statistical estimation and pattern recognition. In this paper we

"... Principal component analysis (PCA) is a ubiquitous technique for data analysis and processing, but one which is not based upon a probability model. In this paper we demonstrate how the principal axes of a set of observed data vectors may be determined through maximum-likelihood estimation of paramet ..."

Principal component analysis (PCA) is a ubiquitous technique for data analysis and processing, but one which is not based upon a probability model. In this paper we demonstrate how the principal axes of a set of observed data vectors may be determined through maximum-likelihoodestimation

"... Cluster analysis is the automated search for groups of related observations in a data set. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures and most clustering methods available in commercial software are also of this type. However, there is little ..."

for model-based clustering that provides a principled statistical approach to these issues. We also show that this can be useful for other problems in multivariate analysis, such as discriminant analysis and multivariate density estimation. We give examples from medical diagnosis, mineeld detection, cluster